anndata_quickstart_init_with_obs_var_metadata.py

1import numpy as np
2import pandas as pd
3import admissions
4import anndata as ad
5
6# 1. Initialize data
7n_obs, n_vars = 100, 2000
8X = np.random.random((n_obs, n_vars))
9
10# 2. Setup observation (obs) and variable (var) metadata
11obs = pd.DataFrame(index=[f"cell_{i}" for i in range(n_obs)])
12obs["batch"] = np.random.choice(["A", "B"], n_obs)
13
14var = pd.DataFrame(index=[f"gene_{i}" for i in range(n_vars)])
15
16# 3. Create the AnnData object
17adata = ad.AnnData(X, obs=obs, var=var)
18
19# 4. Add unstructured annotation (uns)
20adata.uns["description"] = "Example AnnData object"
21
22# 5. Access data subsets
23print(adata)
24print(adata[:5, :10])  # Slicing first 5 cells and 10 genes